Plexin d1 as a target for tumor diagnosis and therapy

ABSTRACT

The present invention relates to plexin D1 for use as a targetable protein in the treatment or diagnosis of disorders that involve expression of plexin D1. Diagnosis is suitably effected by detecting the presence of plexin D1 in the body or a bodily tissue or fluid, whereas treatment is effected by targeting plexin D1 for delivery of therapeutics to the site where treatment is needed. The invention further relates to the use of molecules that bind plexin D1, a nucleic acid encoding plexin D1 or a ligand of plexin D1 for the preparation of a therapeutical composition for the treatment or diagnosis of disorders that involve expression of plexin D1. The disorders comprise disorders in which plexin D1 is expressed on tumor cells, tumor blood vessels or activated macrophages.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/210,676, filed Jul. 14, 2016, pending, which is a divisional of U.S.patent application Ser. No. 13/541,296, filed Jul. 3, 2012, now U.S.Pat. No. 9,422,358, issued Aug. 23, 2016, which is a continuation ofU.S. patent application Ser. No. 11/996,166, filed Mar. 3, 2008,abandoned, which is a national stage entry of International PatentApplication Serial No. PCT/EP06/07241, filed Jul. 20, 2006, whichpublished as PCT Publication No. WO 2007/009816 on Jan. 25, 2007, whichclaims benefit of European patent application Serial No. 05076675.7,filed Jul. 21, 2005, the disclosure of each of which is herebyincorporated herein in its entirety by this reference.

TECHNICAL FIELD

The present invention relates to the identification of a noveltargetable protein that can be used in the treatment and diagnosis oftumors, in particular, solid tumors, and disorders that involveinflammation, in particular, rheumatoid arthritis, atherosclerosis andmultiple sclerosis.

BACKGROUND

To grow beyond a size of 2-3 mm³, tumors have to recruit aneovasculature via angiogenesis. Tumors accomplish this via expressionof Vascular Endothelial Growth Factor-A (VEGF-A), either induced byhypoxia in the tumor center or as a result of malfunctioning tumorsuppressor gene products or activated proto-oncogenes. A number ofcompounds that target the VEGF-A signaling pathway has been developedwith the aim to inhibit angiogenesis and, consequently, tumor growth.Although such anti-angiogenic therapies have been effective in animaltumor models, translation to the clinical level has so far proven to beless successful (M. E. Eichhorn et al., Drug Resist. Update 7:125-138(2004)).

For this, there is a number of possible explanations. In clinicallyrelevant situations, tumors may have been growing for months or evenyears at the time of diagnosis, and a significant proportion of thevasculature may be more or less mature and thus insensitive toangiogenesis inhibition. This situation is in sharp contrast to that inmost animal models in which, as a rule, aggressive, fast-growing tumorsare studied. Furthermore, patients that are candidates foranti-angiogenic therapy are typically patients with disseminated,uncontrollable cancer and growth of metastases may not always bestrictly dependent on angiogenesis. Because most metastases areblood-borne, they grow out in organs with intrinsically high vesseldensities like liver, lung and brain, where they can grow in anangiogenesis-independent fashion by co-option of pre-existent vessels.

Indeed, an angiogenesis inhibitor that very effectively inhibits tumorgrowth in a number of subcutaneous tumor models (S. R. Wedge et al.,Cancer Res. 62:4645-4655 (2002)) does not inhibit growth of infiltrativetumors in mouse brain. Moreover, upon treatment of mice carrying highlyangiogenic brain tumors, angiogenesis inhibition did not result in ahalt of further tumor progression, but rather in a progression after aphenotypic shift toward co-option and infiltration (W. P. Leenders etal., Clin. Cancer Res. 10:6222-6230 (2004)). These results imply thatanti-angiogenic therapy should be supplemented by vascular targetingtherapies in which the existing tumor vascular bed is attacked,resulting in secondary tumor cell death due to disruption of the tumor'sblood supply.

To accomplish effective vascular targeting therapy, markers have to beidentified that have specificity for tumor vasculature. Much effort hasalready been put in this, but with varying success. Effective vasculartumor targeting has been accomplished using single chain antibodies,directed against the fibronectin ED-B domain, which is selectivelyexpressed and deposited in the extracellular matrix of newly formedvessels in angiogenic tumors (M. Santimaria et al., Clin. Cancer Res.9:571-579 (2003)). Targeting of a_(v)β₃-integrin (the expression ofwhich is restricted to immature vessels) using RGD peptides or Vitaxinyielded a disappointing result, whereas endoglin-expression was notspecific for tumor blood vessels (J. A. Posey et al., Cancer Biother.Radiopharm. 16:125-132 (2001); E. Balza et al., Int. J. Cancer94:579-585 (2001)).

In inflammatory diseases such as rheumatoid arthritis (RA) oratherosclerosis, angiogenesis and activation of the vasculature is alsooften part of the pathology. The vasculature here paves the way forinflammatory cells to extravasate and exert their destructive action.Such diseases can thus also benefit from targeting to blood vessels.

BRIEF SUMMARY

It is, therefore, the object of the present invention to provide a newtargetable protein that can be used in the treatment and diagnosis ofcancer and inflammatory diseases or diseases that involve inflammation.

In the research that led to the present invention, it was found thatplexin D1 is expressed on the luminal side of endothelial cells in tumorblood vessels, on the tumor cells themselves and on activatedmacrophages that are found in tumors, in inflammation and inatherosclerotic plaques.

The invention thus relates to plexin D1 for use as a targetable proteinin the treatment or diagnosis of disorders that involve expression ofplexin D1.

The plexin family of receptors consists of four classes (PLXNA-D) andnine members in mammals. Plexins comprise a family of large, single-passmembrane proteins with homology to scatter factor receptors, encoded bythe MET gene family. Members of the plexin family share Sema domains,Met-related sequences (MRS), a transmembrane region and intracellularmotifs that are predictive of Rac/Rho-GTPase signaling (FIG. 1).

Since signaling via GTPases results in cytoskeletal rearrangements,events that are critically involved in formation of filopodia andlammelipodia and cellular migration, plexins can be regarded asregulators of migration.

Plexins are receptors for the semaphorins, a family of secreted,GPI-anchored or transmembrane proteins that is subdivided in sevensubclasses. Each plexin has its own (set of) semaphorin bindingpartners, and each plexin-semaphorin combination results in a specificresponse. Class 3 semaphorins are potent axon repellants and are as suchinvolved in morphogenesis of the nervous system (for review, see, R. J.Pasterkamp et at., Curr. Opin. Neurobiol. 13:79-89 (2003); H. Fujisawa,J. Neurobiol. 59:24-33 (2004)). For activation of plexins by thesemaphorins, additional plexin binding partners may be required. Thesebinding partners, neuropilin-1 and -2 (NP-1 and NP-2) have no signalingmotifs in the intracellular domain and are thought of as passiveco-receptors, enabling the interaction between sempahorins and plexins.

Some plexins form yet larger membrane complexes with and activatesignaling receptors as Off Track (Otk) and the scatter factor receptorsMet and Ron. A direct interaction between plexin A1 and the angiogenicVascular Endothelial Growth Factor-receptor-2 (VEGFR2) has also beendemonstrated (T. Toyofuku et al., E-publication in Genes Dev. 18:435-447(2004)). Because NP-1 binds to plexin family members but also to VEGFR2,it is conceivable that multicomponent membrane protein complexes existthat encompass VEGFR2, NP-1 and plexins, establishing a link betweenplexins and angiogenesis (see also B. M. Weinstein, Cell 120:299-302(2005)).

Neuropilins are also co-receptors for the potent angiogenic factorVascular Endothelial Growth Factor-A (VEGF-A₁₆₅) and enhance itsaffinity for VEGFR2. Interestingly, the VEGF-A₁₆₅ binding site on NP-1overlaps with that for semaphorin 3A (H. Q. Miao et al., J. Cell. Biol.146:233-242 (1999)). It has been postulated that VEGF-A binding to NP-1promotes migration of endothelial cells by competing for binding ofclass 3 semaphorins, which is generally followed by F-actindepolymerization and repulsion of cell extensions (R. E. Bachelder,Cancer Res. 63:5230-5233 (2003)). Similar antagonistic behavior ofVEGF-A and class 3 semaphorins have been described in a neuronalprogenitor cell line (D. Bagnard et al., J. Neurosci. 21:3332-3341(2001)) and tumor cells (Bachelder (2003), supra). Since antagonisticeffects were observed in tumor cells that are devoid of VEGF receptors,it is conceivable that the underlying mechanism involves members of theplexin family, establishing a further link between plexins and VEGF-Asignaling.

The present inventors have previously found that the family memberplexin D1 (plxnD1) is not only expressed in neuronal cells, but also inendothelial cells of the vasculature during early stages of development(B. van der Zwaag et al., Dev. Dyn. 225:336-343 (2002)), an observationthat was confirmed by two other groups (A. D. Gitler et al., Dev. Cell.7:107-116 (2004); J. Torres-Vazquez et al., Dev. Cell, 7:117-123(2004)). In adult vasculature, plxnD 1 is absent. Plxnd1-knockout miceand zebrafish carrying mutations in the plxnd1 gene are characterized bymaldevelopment of the cardiovascular system (A. D. Gitler et al. (2004),supra; J. Torres-Vazquez et al., (2004), supra). Neuropilin-1 (NP-1) andNP-1/Neuropilin-2 (NP-2) double knock-out mice also suffer from lethaldefects in vascularization and aortic arch malformations duringembryonic development (T. Kawasaki et al., Development 126:4895-4902(1999); S. Takashima et al., Proc. Natl. Acad. Sci. U.S.A. 99:3657-3662(2002); C. Gu et al., Dev. Cell. 5:45-57 (2003)).

Furthermore, morpholino-mediated knock-down of NP-1 in zebrafish leadsto maldevelopment of intersegmental vessels and, in this model system, aclear link between NP-1 and VEGF-A₁₆₅ has been established. (P. Lee etal., Proc. Natl. Acad. Sci. U.S.A. 99:10470-10475 (2002)). Theresemblance of the phenotypes of plxnd1, neuropilin-1 and semaphorin 3Cknock-out mice (L. Feiner et al., Development 128:3061-3070 (2001)) isconsistent with the finding that Plexin D1 is a neuropilin-1-dependentreceptor for semaphorin 3C (A. D. Gitler et al. (2004), supra). However,PlxnD 1 is also a receptor for semaphorin 3E, and this interaction doesnot require neuropilins for Semaphorin 3E-mediated signaling (C. Gu etal., Science 307:265-268 (2005)).

According to the invention, it was now found that plexin D1 is alsoinvolved in angiogenesis during tumor growth and is expressed on theluminal side of endothelial cells in tumor blood vessels. Plexin D1 wasfurthermore found to be expressed by activated macrophages. Plexin D1was also found to be expressed on tumor cells in a wide variety of tumortypes.

The present invention thus relates to plexin D1 for use as a targetableprotein in the treatment or diagnosis of disorders that involveexpression of plexin D 1.

Diagnosis is effected by detecting the presence of plexin D1 or a plexinD1-encoding nucleic acid in the body or a bodily tissue or fluid.

Treatment is effected by targeting plexin D1 for delivery oftherapeutics to the site Where treatment is needed, by interfering inthe interaction between plexin D1 and its ligands, by interfering in theexpression of the plexin D1 gene or by capturing plexin D 1 ligands toinhibit interaction with plexin D1.

The invention thus furthermore relates to the use of molecules that bindplexin a nucleic acid encoding plexin D1 or a ligand of plexin D1 forthe preparation of a therapeutical composition for the treatment ordiagnosis of disorders that involve expression of plexin D 1. All thesemolecules will be identified herein as “binding molecules” or “bindingentities.”

The disorders comprise, in particular, disorders in Which plexin D1 isexpressed on tumor cells, tumor blood vessels or activated macrophages.

The tumor cells on which plexin D1 is expressed comprise brain tumors,in particular, astrocytomas, oligodendrogliomas and hemangioblastomas,colon carcinomas, in particular, ductal carcinomas of the colon,prostate carcinomas, renal cell carcinomas, in particular, renal clearcell carcinomas, mamma carcinomas, in particular, ductal carcinomas ofthe breast, ovary carcinomas, squamous cell carcinomas, melanomas, lungcarcinomas, in particular, small-cell lung carcinomas and non-small-celllung carcinomas, soft tissue sarcomas, etc.

When the disorders that are treated according to the invention areinflammatory diseases, they are, in particular, autoimmune disease, morein particular, rheumatoid arthritis, or they are atherosclerosis ormultiple sclerosis.

Molecules that bind plexin D1 are, for example, selected fromantibodies, antibody fragments, proteins, protein domains, peptides, andsmall molecules. These molecules can be used to target plexin.

Molecules that bind the nucleic acid encoding plexin D1 are, forexample, oligonucleotides, such as RNA or DNA aptamers, for example,selected from siRNA, antisense RNA, and antisensephosphothio-oligonucleotides. These molecules can be used to interferewith the expression of plexin D1.

Molecules that bind a plexin D1 ligand are, for example, selected fromantibodies against ligands, the soluble ectodomain of plexin D1 or smallmolecules, such as peptides, that bind plexin D1 ligands. Thesemolecules can be used to capture circulating plexin D1 ligand, preventbinding of the ligand to plexin D1 on tumor vessel cells, tumor cells oractivated macrophages and interfere with the function of plexin D1 onthese cells.

For diagnosis, the binding molecule is suitably labeled with adetectable marker. Such a detectable marker is, for example, selectedfrom a radioactive label, paramagnetic label, a fluorescent label, and achemiluminescent label. Diagnosis can be performed in a sample of abodily fluid or tissue in viva, in situ or ex viva. Examples ofdiagnostic techniques are in situ hybridization of, for example, plexinD1 mRNA or immunohistochemistry on biopsies or tumor cells.

For treatment, the binding molecule is, for example, provided with anentity that damages or kills the tumor cell and/or the tumor endothelialcell, in particular, a cytotoxic entity, such as a radionuclide, atoxin, boron for Boron Neutron Capture Therapy (BNCT), or a prodrug thatis coupled to the binding entity via a cleavable linker, which isactivated in response to cleavage of that linker, or apoptosis-inducingpeptides, an example of which is the (KLAKLAK)₂ (SEQ ID NO:7) sequence.Such peptides are added to the binding entity by molecular geneticengineering techniques.

The entities described above may be directly conjugated to the bindingentity, they may be present in nanodevices, such as liposomes orpolymersomes, that are conjugated to the binding entity.

Boron Neutron Capture Therapy (BNCT) comprises irradiation of a diseasedarea, such as a tumor or an inflammation, in which boron has accumulatedafter intravenous injection of the liposomal conjugate, with neutrons,after which boron atoms will decay to lithium under emission ofdestructive alpha particles.

Alternatively, therapy may be effected by inducing local thrombosis inthe tumor vessels to block the blood supply to the tumor and induce celldeath. An example of such molecule is Tissue Factor (TF).

Advantageously, plexin D1 can be targeted with specific bindingmolecules upon intravenous administration since plexin D1 is expressedon the luminal side of endothelial cells in tumor blood vessels.Therapeutic compounds for damaging or killing tumor cells that arecoupled to the binding molecule can reach the tumor from within andcompounds that induce thrombosis are easily delivered to their site ofaction.

Interference with plexin D1 function represents a way to inhibitangiogenesis, to inhibit tumor cell migration, and to inhibit macrophagemigration. Thus, the invention provides methods of treating orsuppressing disorders in which plexin D1 is involved, by using thespecific presence of plexin D1 to deliver therapeutics locally todiseased tissues, and/or by interference in the function of plexin D1 orin the interaction between plexin D1 and its ligands.

The invention is thus based on the fact that plexin D1 can be used as atargetable marker on tumor blood vessels, as a targetable proteininvolved in tumor angiogenesis, as a targetable marker on tumor cells,and as a targetable protein involved in cellular migration.

The invention thus also relates to the use of molecules that bind toplexin D1, its gene or mRNA or its ligands in diagnosis and therapy. Allkinds of specific binding molecules, and derivatives thereof can be usedin the invention, in particular, proteinaceous compounds, such as, butnot limited to, antibodies, antibody fragments, single-domain antibodyfragments, other proteinaceous binding domains, such as, but not limitedto, lipocalins, and small molecules that specifically bind plexin D1 orits ligands. For binding to the plexin D1 gene or the mRNA transcribedfrom the plexin D1 gene, nucleic acid molecules, such as DNA or RNA,aptamers can be used.

In a first embodiment of the invention, plexin D1 or plexin D1 ligandbinding molecules are antibodies, in particular, monoclonal antibodies,more in particular, human or humanized antibodies in which the constantregions of the original antibody are substituted with the constantregions of human antibodies, or fragments thereof, which still bind toplexin D1 or its ligand.

The antibody is preferably a human IgG1 antibody. However, other humanantibody isotypes are also encompassed by the invention, including IgG2,IgG3, IgG4, IgM, IgA1, IgA2, IgAsec, IgD, and IgE. Also, allanimal-derived antibodies of various isotypes can be used in theinvention.

The antibodies can be full-size antibodies or antigen-binding fragmentsof antibodies, including Fab, F(ab′)₂, single-chain Fv fragments, orsingle-domain VHH, VH or VL single domains.

Preferably, antibodies against plexin D1 are human monoclonal antibodiesproduced by a hybridoma cell, which includes a B cell obtained from animmunized transgenic animal having a genome comprising a human heavychain transgene and a human light chain transgene, fused to animmortalized cell, or an animal-derived antibody or antibody fragmentproduced by a hybridoma cell, which includes a B cell obtained from animmunized animal, fused to an immortalized cell, or human and animalantibodies, produced by a eukaryotic cell transfected with the cDNA orgenomic DNA encoding the antibody or antibody fragment.

In a preferred embodiment of the present invention, single-domain (VHH)Llama antibodies with affinity to plexin D1 are provided, morespecifically, Llama single-domain antibodies A12 (SEQ ID NO:1.) and F8(SEQ ID NO:2), either or not displayed on M13 bacteriophages, also knownto those with skill in the art as phage-display VHH antibodies.

A preferred single-chain antibody is derived from antibody 11F5H6 and17E9C12. The sequence of the single-chain antibody is shown in SEQ IDNO:3 and SEQ ID NO:4.

The antibodies for use according to the invention may be high-affinityantibodies, which are evoked in non-transgenic laboratory animals, or ina transgenic animal in which the endogenous globulin locus has beensubstituted for the human globulin locus, thus allowing production ofhuman antibodies in such animals (A. Jakobovits, Curr. Opin. Biotechnol.6:561-566 (1995)).

The invention further relates to a method of producing the antibodies ofthe invention, comprising immunizing an animal with plexin D1, or a cellexpressing plexin D1, or a nucleic acid encoding plexin D1, or parts ofthe extracellular domain of plexin D1, such that antibodies againstplexin D1 are produced by the B cells of the animal, isolating the Bcells from the animal and fusing the B cells to a myeloma cell line toobtain immortalized cells that secrete the antibody. The animal ispreferably a transgenic animal having a genome comprising a human heavychain transgene and a human light chain transgene so that the resultingantibody is humanized.

In one embodiment, the method includes immunizing a laboratory animalwith a synthetic peptide, chosen from the plexin D1 extracellulardomain, for example, peptide 47-63 corresponding to the amino terminusof the mature plexin D1 amino acid sequence. Immunizations are, however,preferably done with recombinant extracellular domains, preferably aregion with low similarity to other family members of the plexins, forexample, a region comprising amino acids 47-546, lacking theMet-Related-Sequences. The recombinant plexin D1 extracellular domainscan be produced in E. coli cells by inserting the coding nucleic acidsin a suitable prokaryotic expression vector, for instance, under controlof the β-galactosidase promoter, transformation of E. coli cells withthe vector, and isolation of the recombinant proteins from purifiedinclusion bodies. It is preferred, however, that antibodies are evokedby immunization with the recombinant plexin D1 extracellular domain thatis produced by eukaryotic cells, therefore, containingpost-translational modifications that are most similar to those presentin native plexin D1, for example, by Chinese hamster ovary (CHO) cellsafter transfection with a vector, containing the coding nucleic acidsfor the extracellular domains under the control of a cytomegaloviruspromoter. Recombinant extracellular plexin D1 fragments may or may notbe fused to tags facilitating purification, e.g., a VSV tag or aconstant region of a heavy chain of an immunoglobulin.

The method of producing the antibody may also comprise cloning theantibody coding regions from plexin D1-specific B-cells into anexpression vector and expressing the coding sequence. In a preferredembodiment, the expression vector is pHENIXHISVSV, enabling expressionby E. coli host cells of the antibody, flanked at the carboxyterminalend by a Vesicular Stomatis Virus (VSV-tag) and a His*8 tag. The VSV tagis meant to facilitate immunohistochemical detection, using specificantibodies. The His*8 tag is meant to facilitate purification based onNickel affinity chromatography. Other expression vectors can likewise beused.

More specifically, the invention provides an isolated single-domainantibody A12, having a dissociation constant of less than 2×10⁻⁸ M,which binds to the amino terminus of plexin D1 and which detects plexinD1 in immunohistochemical stainings and homes to plexin D1-expressingtumor blood vessels, and also to an isolated single-domain antibody F8,having a dissociation constant of less than 3×10⁻⁸ M, which binds to theamino terminus of plexin D1 and which detects plexin D1 inimmunohistochemical stainings and homes to plexin D1-expressing tumorblood vessels. Both isolated single-domain antibodies may be fused tothe constant region of a human IgG1 heavy chain or the constant regionof a mouse IgG1 heavy chain.

Preferably, fully human antibodies are used within the scope of theinvention. In another embodiment, humanized or laboratory animal-derivedantibodies may be used.

The invention further provides bispecific antibodies that have a bindingspecificity for plexin D 1, and a binding specificity for a humanantigen-presenting cell, or for an Fe receptor, wherein the Fe receptoris a Fe(gamma)R1 or a human Fe(alpha) receptor.

The invention also provides nucleic acid molecules encoding thepreferred antibodies, or antigen-binding portions. Recombinantexpression vectors that include nucleic acids that encode the antibodiesof the invention, as well as host cells transfected with such vectors,are also encompassed in the invention.

Other binding molecules for use in the invention are small moleculesthat specifically bind to Plexin D1. The term “small molecule” refersoften to molecules with molecular weights of 500 or below. The term iscommonly used these days and thus clear to the skilled person. Moreover,small molecule libraries are already available or are being developed.An example of such library is the NIH Molecular Libraries Small MoleculeRepository (MLSMR). Such libraries are subjected to High ThroughputScreening (HTS) to identify molecules that bind to plexin D1. Theinvention also relates to the small molecules that result from a screenof such libraries.

Other compounds that can be used according to the invention comprisepeptides or aptamers (Ulrich, Med. Chem. 1(2):199-208 (2005)) that bindto extracellular domains of plexin D1 and thereby interfere with bindingof plexin D1 ligands to plexin D1. Conversely, such peptides or aptamersmay also bind to the plexin D1 binding sites of the plexin D1 ligandsand thereby interfere with ligand binding to plexin D1.

For interfering with the expression of the plexin D1 gene, another typeof binding molecule is used, in particular siRNA, antisense RNA orantisense phosphothio-nucleotides. Small interfering RNA (siRNA)comprises small strands of RNA that interfere with the translation ofmessenger RNA. SiRNA binds to the complementary portion of the targetmessenger RNA and tag it for degradation, thus inhibiting geneexpression. This is commonly known as gene “silencing.” SiRNA is usually21 to 23 nucleotides long. Antisense RNA is an RNA molecule transcribedfrom the coding, rather than the template, strand of DNA, so that it iscomplementary to the sense mRNA. Formation of a duplex between the senseand antisense RNA molecules blocks translation and may also subject bothmolecules to double-strand-specific nucleases, thus inhibitingexpression of the gene. Inhibition of expression of the gene can be usedto block angiogenesis and migration of tumor cells and macrophages.

Preferably, the above-described binding molecules bind to plexin D1, itsgene or its ligand in eukaryotic cells. The molecules specificallyaccumulate in tumors upon intravenous injection or specificallyaccumulate in tumor blood vessels upon intravenous injection.

The antibodies, fragments thereof, small molecules and otherproteinaceous compounds that all bind plexin D1 can be used in variousways.

In one embodiment, the invention relates to compounds that bind to theextracellular part of plexin D1, which binding results in interferenceof plexin D1 function, Alternatively, the invention relates to compoundsthat bind to the intracellular domain of plexin and that preventsignaling by plexin D1.

In a specific embodiment, such binding molecules bind to plexin D1 tointerfere with the formation of multicomponent membrane complexes byinhibiting binding of plexin D1 ligands, in particular, neuropilin-1,neuropilin-2, semaphorin 3C, sempaphorin 3E, VEGF-receptor-1,VEGF-receptor-2 or VEGF-A, to plexin D1. Such binding molecules lead toinhibition of ligand-induced GTPase signaling by plexin D1 or toinhibition of migration of cells expressing plexin D1, in particular,tumor-associated endothelial cells, tumor cells or macrophages.

According to another aspect thereof, the invention relates to a methodof inducing lysis of a cell expressing plexin D1, comprising contactinga cell expressing plexin with the binding molecules, in particular, theantibodies, of the invention in the presence of human effector cells,such that lysis of the cell expressing plexin D1 occurs.

In a still further embodiment, the binding molecule is combined with orcoupled to an effector compound that can detect the presence of plexinD1 for diagnostic purposes or that can perform an effect on the cellexpressing plexin D1. The diagnostic or therapeutic effector compoundcan be directly coupled to the binding molecule or can be present in atransport vehicle, such as a nanodevice, in particular, a liposome orpolymersome, that is coupled to the binding molecule. Alternatively, thebinding molecule can be a bispecific antibody that binds both plexin D1and the effector compound, thus targeting the effector compound to asite or cell where plexin D1 is expressed.

The invention thus provides in a particular embodiment thereof the useof such binding molecules in a method of diagnosing a disease mediatedby expression of plexin D1, which method comprises intravenous deliveryof the proteinaceous, aptameric or small molecule plexin D1 bindingmolecules, conjugated to an effector compound allowing in vivo detectionof the binding molecules.

Diagnostic effector compounds are, for example, radioisotopes orcontrast agents for Magnetic Resonance Imaging (MRI), such asgadolinium-DTPA, or fluorescent dyes.

Examples of radioactive substance comprise, but are not limited to,technetium^(99m) (^(99m)Tc), iodine-123 (¹²³I), iodine-131 (¹³¹I),rhenium-186 or -188 (^(186/188)Re), gallium-67 (⁶⁷Ga), thebeta-radiation emitting substances yttrium-90 (⁹⁰Y) or lutetium-177(¹⁷⁷Lu), and the positron emitting isotopes Fluorine-18 (¹⁸F) andCarbon-11 (¹¹C). Such radioisotopes can be used to either detect ordamage or kill cells expressing plexin D1. Usually, different isotopesare used for diagnosis and therapy. The skilled person is well aware ofwhich isotope to use for which tissue and for which type of use.

In another embodiment, the proteinaceous, aptameric and small molecularbinding molecules for use in the invention can be combined with orcoupled to a toxic agent, such as chemotherapeutic agent either directlyor in a transport, vehicle, in particular, a nanodevice, such as aliposome or polymersome.

In another embodiment, a plexin D1 binding entity of the invention iscoupled to one or more chemotherapeutic agents selected from the groupconsisting of nitrogen mustards (e.g., cyclophosphamide and ifosfamide),aziridines (e.g., thiotepa), alkyl sulfonates (e.g., busulfan),nitrosoureas (e.g., carmustine and streptozocin), platinum complexes(e.g., carboplatin and cisplatin), non-classical alkylating agents(e.g., dacarbazine and temozolamide), folate analogs (e.g.,methotrexate), purine analogs (e.g., fludarabine and mercaptopurine),adenosine analogs (e.g., cladribine and pentostatin), pyrimidine analogs(e.g., fluorouracil (alone or in combination with leucovorin) andgemcitabine), substituted ureas (e.g., hydroxyurea), antitumorantibiotics (e.g., bleomycin and doxorubicin), epipodophyllotoxins(e.g., etoposide and teniposide), microtubule agents (e.g., docetaxeland paclitaxel), camptothecin analogs (e.g., irinotecan and topotecan),enzymes (e.g., asparaginase), cytokines (e.g., interleukin-2 andinterferon-[alpha]), monoclonal antibodies (e.g., trastuzumab andbevacizumab), recombinant toxins and immunotoxins (e.g., recombinantcholera toxin-B and TP-38), cancer gene therapies, and cancer vaccines(e.g., vaccine against telomerase).

Chemotherapeutic agents are preferably selected from the groupconsisting of doxorubicin, cisplatin, bleomycin sulfate, carmustine,chlorambucil and cyclophosphamide hydroxyurea. Other compounds are knownto the person skilled in the art.

A tumor can also be treated by blocking its blood supply by inducinglocal thrombosis in the tumor vasculature. The binding molecules of theinvention can, in this embodiment, be used to target,thrombosis-inducing molecules, such as the blood coagulation co-factorTF (Tissue Factor), a radioactive entity or a toxin, such as ricin tothe site of the tumor. Effector compounds can be coupled to the bindingmolecule, in particular, a plexin D1 binding molecule, or can be presentin a nanodevice, such as a liposome or polymersome, that is coupled tothe plexin D1 binding molecule.

An alternative method of treating cancer or an inflammatory disorderaccording to the invention is with boron. The binding molecules of theinvention can be conjugated to transport vehicles, in particular,nanodevices, such as liposomes or polymersomes, that are filled withboron to obtain a therapeutic composition. After delivery andaccumulation of this composition in the diseased area, this area isirradiated with neutrons, resulting in emission of radioactive andcytotoxic alpha-particles that damage or kill the tumor endothelialcells, tumor cells and/or activated macrophages.

It is desirable for tumor blood vessel targeting antibodies to have highaffinities toward plexin D1, for example, higher than 10⁻⁸, preferablyhigher than 10⁻⁹, more preferably higher than 10⁻¹⁰ M. High affinity andthe high molecular weight of antibodies will, however, restrictpenetration into tumor tissue. Therefore, the nucleic acids that encodethe monoclonal antibodies obtained via RT-PCR cloning, can be used togenerate antibody derivatives, for example, antibodies that lack theconstant region and are monovalent, or antibody fragments that areadapted to optimal affinities for blood vessel targeting or tumorpenetration by mutagenic procedures. These antibody derivatives willhave lower affinities and lower molecular weight and will have improvedtumor cell targeting properties.

Different binding molecules of the invention can be combined in amixture. In a specific embodiment, the members of the mixture have avarying affinity. An example of such a combination is a mixture ofmonoclonal antibodies and/or antibody fragments or a mixture ofantibodies with small molecules. The monoclonal antibodies having highaffinity can be used for targeting vessels, whereas the smallerfragments having a lower affinity are better able to penetrate and reachthe tumor cells. Alternatively, a mixture of plexin D1 binding moleculescan be used together with plexin D1 ligand binding molecules and/or withmolecules that bind nucleic acids encoding plexin D1, or plexin D1ligand binding molecules can be combined with molecules that bindnucleic acids encoding plexin D1.

The plexin D1 binding molecules of the invention can be used in a methodof treating a disease mediated by expression of plexin D1, comprisingintravenous delivery of the binding molecules of the invention at a doseeffective in treating that disease.

The binding molecules can also be used in a method of diagnosing adisease mediated by expression of plexin D1, comprising intravenousdelivery of conjugates of plexin D1 binding molecules with aparamagnetic, fluorescent or radioactive tracer followed by magneticresonance imaging, optical imaging, SPECT or PET.

The binding molecules can further be used in a method of treating orsuppressing a disease mediated by expression of plexin D1, comprisingintravenous delivery of the proteinaceous and small molecular bindingmolecules of the invention or a composition of proteinacous and smallmolecular binding molecules.

The disease to be treated or diagnosed can be cancer, an inflammatorydisease, in particular, an autoimmune disease, such as rheumatoidarthritis, or atherosclerosis, or multiple sclerosis.

Diagnosis can be performed in vivo and in vitro. An in vivo method isdescribed above and can be performed with magnetic resonance imaging(MRI) or with SPECT or PET cameras after accumulation of theradioactively labeled binding molecule in the diseased tissue.

Another diagnostic method comprises detecting the presence of plexin D1in a sample in vitro or ex vivo. Such method comprises contacting thesample with binding molecules of plexin D1, or nucleic acids that bindthe plexin D1 gene or its mRNA or a copy DNA derived from this mRNA, allbound to a detectable marker, under conditions that a complex betweenthe antibody and plexin D1 forms, and detecting the formation of thecomplex. The complex can be detected by visualizing the detectablemarker. Samples can be bodily fluids, such as blood, serum, plasma,saliva, urine, semen, feces, or tissues, such as biopsies of tumorcells.

The invention further relates to an expression vector, comprising thecoding sequence for Llama antibody F8 or A12, or for the single-chainantibody derived from antibody 11F5H6 and suitable regulatory sequences.The invention also relates to a cell transfected with the expressionvector. The invention further relates to the recombinant proteinobtainable by expressing the expression vector.

Another aspect of the invention relates to an expression vector,comprising the coding sequence for the extracellular domain of plexinD1, optionally fused to a constant region of a human heavy chain andsuitable regulatory sequences. The invention also relates to a celltransfected with the expression vector. The invention further relates tothe recombinant protein obtainable by expressing the expression vector.

The recombinant protein comprises the extracellular domain of plexin D1,which binds to plexin D1 ligands and thus prevents binding of theligands to cell-associated plexin D 1. Preferably, the coding sequencecodes for a recombinant protein comprising amino acids 47-506 of theextracellular domain of plexin D1, which binds to plexin D1 ligands andthus prevents binding of the ligands to cell-associated plexin D1, oramino acids 507-1274 of the extracellular domain of plexin D1, whichbinds to plexin D1 ligands and thus prevents binding of the ligands tocell-associated plexin D1. Such recombinant protein may carry mutationsthat increase the affinity for plexin D1 ligands and thereby havingincreased potency as decoy receptor. Such mutations are usually inducedby making changes in the coding sequence used for producing therecombinant protein.

The invention further relates to the use of the binding molecules of theinvention in a method of treating or suppressing a disease mediated byplexin D1, comprising intravenous or intratumoral delivery of decoyplexin D1 extracellular domains as described above, or in a method oftreating or suppressing a disease mediated by plexin D1, comprisingintravenous delivery of adenoviruses or lentiviruses, containing thecoding nucleotides for the recombinant extracellular domains of plexinD1 or parts thereof as described above.

These antagonistic decoy plexin D1 receptors interfere with theinteraction between plexin D1 and its ligands, in particular,neuropilin-1, semaphorin 3C and sempahorin 3E, and thereby interferewith plexin D1 function.

Preferably, the decoy plexin D1 receptors have increased affinity towardplexin D1 ligands, as compared to plexin D1. Such increased affinity maybe obtained by creating a library of plexin. D1 extracellular domains,carrying at random introduced mutations, and selecting decoy receptorswith most potent antagonistic behavior in cell migration assays.

In order to produce the proteinaceous molecules (including peptides,polypeptides and glycosylated polypeptides or polypeptides having otherpost- or peritranslational modifications), it is desirable to insert therecombinant nucleic acid that encodes fragments of the extracellulardomain of plexin D1 that comprise the binding sites for semaphorin 3C,semaphorin 3E and NP-1 into expression vectors. The antagonistsaccording to the invention are preferably produced from a nucleic acidor an expression vector according to the invention, preferably in a hostcell.

The molecules of the invention may also be used in a combination oftreatment methods as described above and/or with conventional therapiesor anti-angiogenic therapy for further preventing the formation of atumor neovasculature, or radiotherapy and/or adjuvant chemotherapy.

The invention further relates to a method of identifying molecules thatare capable of binding to plexin D1, which method comprises contacting acollection of molecules with plexin D1 and selecting the molecules fromthe collection that show binding to plexin D1 as plexin D1 bindingmolecules. The collection of molecules can, for example, be present insmall molecule libraries, on a protein array, etc. The techniques forscreening collections of molecules are in itself known. The inventionresides in the identification of the target that is to be bound, whichis plexin D1.

this disclosure, the term “binding molecule” is used for all types ofbinding molecules, i.e., the ones that bind plexin D1, the ones thatbind a nucleic acid encoding the plexin D1 gene, and the ones that bindplexin D1 ligands. All these types of molecules can be coupled toeffector compounds as described above.

BRIEF DESCRIPTION OF THE FIGURES

The present invention will be further illustrated in the Examples thatfollow and that are in no way intended to limit the invention. In theExamples, reference is made to the following figures:

FIG. 1: Structural domains of plexin family members: four subfamilieshave been identified, named PlexinA-PlexinD. Horizontally hatched boxesindicate Sema domains, diagonally hatched boxes indicate Met-relatedsequences (MRS) motifs, and the clear box indicates the atypical MRSmotif of PLXND1. PlexinB subfamily members have a potential furin-likeproteolytic site, marked by a grey ribbon. The transmembrane region ismarked by a shaded box and is followed by two conserved intracellulardomains, together comprising the SP-domain, marked by two ovals.

FIG. 2: Panel A) In situ hybridization analysis of cerebralMe157-VEGF-A₁₆₅ lesions using a digoxigenin-labeled mouse-specificplxnd1 RNA probe. Tumor vessels are strongly positive (arrows) whereasbrain capillaries, distant from the lesions, are negative (compare theISH profile with the CD34 staining in FIG. 2, Panel B).

FIG. 3: Human PLXND1-specific ISH analyses of glioblastoma multiforme(Panel A), brain metastases of sarcoma (Panel B), melanoma (Panel C) andmammacarcinoma (Panel D). Insets show CD31 stainings of serial sections.Control ISH using sense probes were negative (not shown). Note that inthese tumors, PLXND1 expression is not confined to the blood vessels.Also, in tumor cells, high levels of the PLXND1 transcript are found,t=tumor, V=vessel.

FIG. 4: ISH analysis using a human-specific digoxigenin-labeled RNAprobe (Panel A) and immunohistochemical staining with CD31 (Panel B) ofnormal brain. Note that vessels are abundantly present but these do notexpress the plexin D1 transcript.

FIG. 5: Specificity of phages (Panel A) and corresponding single-domainantibodies (sdabs) (Panel B) A12 and F8 for peptideH₂N-ALEIQRRFPSPTPTNC-CONH₂ (SEQ ID NO:8). In Panel A, 10¹⁰ phages wereallowed to bind to PLXND1-peptide, BSA, human IgG or irrelevant peptideas described in the text. After rigorous washing, bound phages weredetected using an anti-M13 antibody. In Panel B, similar incubationswere performed but now with soluble sdabs. After washing, bound sdabswere detected and semi-quantified via the VSV-G-tag.

FIG. 6: The dissociation constants (Kds) of the binding betweensingle-domain antibodies A12 and F8 were determined using the Biacore2000 (Uppsala, Sweden) biosensor. The sensor chip and protein couplingchemicals were purchased from Biacore AB. PLXND1-peptide-KLH conjugate(27 μg/ml in Na-Acetate, pH 4.0) or BSA (1 μg/ml in Na-Acetate, pH 5.0)was coupled to activated CM5 surfaces usingN-ethyl-N′-(dimethylaminopropyl)carbodiimide, N-hydroxysuccinimide,under conditions recommended by the manufacturer. Unreacted groups wereinactivated by 1 M ethanolamine, pH 8.5.

Kinetic measurements were performed at 25° C. with a flow rate of 10ml/minute in HBS-EP buffer (10 mM Hepes, pH 7.4, 150 mM NaCl, 3 mM EDTA,0.005% surfactant P20). Six concentrations of Ni-affinity-purified sdabs(in the range of 1 mM to 50 μM) were used to determine the dissociationconstants (Kds) of the interaction with the PLXND1-peptide. After eachexperiment, regeneration of the sensor surface was performed with 10 mMNaOH.

Specific binding, defined by binding to a PLXND1-surface minus bindingto a control BSA-surface, was analyzed using the BIAevaluation 4.1software and a 1:1 Langmuir binding model. Affinities of single-domainantibodies A12 and F8 were 2.1×10⁻⁸ M and 3.5×10⁻⁸ M.

FIG. 7: Evaluation of plexin D1 specificity of single-domain antibodies.Panel A shows immunohistochemical staining of the growth plate oftrabecular bone of a mouse embryo (E16.5) with single-domain antibodyA12, utilizing the VSV-G tag for detection of the antibody. The insetshows an in situ hybridization of a similar embryonic structure using amouse-specific digoxigenin-labeled plexin D1 probe. Note the overlap ofplexin D1 in situ hybridization and immunostaining. Panel B is arepresentative example of a Me157-VEGF-A₁₆₅ lesion in brain of a nudemouse. The vasculature, which is also positive in plexin D1 ISH (seealso FIG. 2), is immunopositive with single-domain antibody F8.

FIG. 8: Immunostainings with single-domain antibody A12 on a selectionof human brain tumors. Tumors shown are (Panel A) glioblastomamultiforme, metastases of (Panel B) melanoma (Panel C) mammacarcinomaand Panel D) renal cell carcinoma. The insets in Panels A and B consistof control stainings with anti-VSV antibody only, and show that thetumor staining is specific. Note that vessels and tumor cells are highlyreactive with the antibody.

FIG. 9: Immunostainings with single-domain antibody A12 on a progressionseries of melanoma. Immunostainings were performed on a nevus, adysplastic nevus and horizontal and vertical growth phases of melanoma.Note that only the neoplastic cells express plexin D1.

FIG. 10: Immunostainings with single-domain antibody A12 on sections ofMe157-VEGF-A brain tumors in mice, treated with ZD6474. In untreated orplacebo-treated mice, tumor vessels stain positive with this antibody.However, in ZD6474-treated mice, there is a dose-dependent decrease ofplexin D1 expression. ZD6474 was given orally, once daily, in the dosageas indicated.

FIG. 11: Double immunostainings with the macrophage marker CD68 andsingle-domain antibody A12 on mammacarcinoma. A subpopulation ofmacrophages express plexin D1 as revealed by a staining protein.

FIG. 12: In vivo homing of phage A12, F8 or an irrelevant phage toMe157-VEGF₁₆₅ brain lesions. Tumor-bearing mice were injected with 10¹²phages in the tail vein and, after 5 minutes, mice were anesthetized andsubjected to cardiac perfusion with 15 ml of phosphate-buffered saline.Mice were sacrificed, brains removed and frozen sections were analyzedfor phage content and distribution. Panel A) M13 staining of a frozensection of brain Me 1 57-VEGF₁₆₅ lesions. Phages are clearlyvessel-associated, as evidenced by the anti-CD34 immunostaining on aserial section, shown in Panel B). The arrows point at a CD34-positivevessel, distant from the lesion, which is not highlighted by anti-M13staining. The inset in Panel A shows a control experiment where anirrelevant phage was injected. Panel C) Distribution of sdab F8 afterintravenous injection in tumor-bearing mice. Sdabs are visualized byimmunohistochemistry using an anti-VSV antibody. Note that the sdab isdetected in tumor vessels but not in normal brain capillaries. The insetshows the control experiment where an irrelevant sdab was injected. Aninterstitial localization was observed, consistent with the leaky natureof the vessels in these tumors. Panel D) Quantification of phage homing.Tumor tissue was dissected from 10 μm frozen sections using lasercapture dissection microscopy. Number of colony-forming phages (cfp)were counted after infection of TG1 cells. Twenty-fold more F8 phageswere eluted from tumors than from comparable areas of unaffected braintissue.

FIG. 13: Single-domain antibody homes to tumor vessels that are not perse newly formed. Nude mice were inoculated with a cell suspension of1.5×10⁵ cells of the human glioma xenograft E98, which was obtained froma subcutaneous E98 tumor. After 3 weeks, phages carrying single-domainantibody F8 were injected in the tail vein, and after 5 minutes, micewere anesthetized and subjected to cardiac perfusion using 15 ml ofphosphate-buffered saline. Mice were then sacrificed, brains removed andfixed in formalin. Serial sections were stained with antibodies againstM13 p8 protein (Panel A), the endothelial marker CD34 (Panel B) andglut-1 (Panel C, a marker for pre-existent brain capillaries).Comparison of Panels A, B and C reveals that not only newly formed tumorvessels accumulate phage F8, but also non-dilated brain vessels thatexpress glut-1, and that, therefore, are considered pre-existent brainvessels that had been incorporated in the tumor.

FIG. 14: Effects of extracellular domains of plexin D1 on thedevelopment of tumor vasculature. Double transfectants of the humanmelanoma cell line Me157, expressing VEGF-A₁₆₅ and the extracellulardomain of plexin D1 comprising amino acids 1-850, were injected in theright internal carotid artery of nude mice. After three weeks, the micewere subjected to Gadolinium-DTPA-enhanced magnetic resonance imaging.Panel A shows MR images of two control mice carrying Me157 brain tumorsthat express VEGF-A₁₆₅ only, Panel B shows MR images of brains of twomice carrying the double transfectant. Vascular leakage, as assayed byGd-DTPA extravasation, tends to be less in the double transtectants,suggesting that VEGF-A-induced vascular leakage is counteracted by theplexin D1 ectodomain. More importantly, blood vessels in thedouble-transfected tumors are activated, as indicated by upregulation ofCD34, yet they express glut-1, strongly suggesting that these vesselsare pre-existent vessels that are incorporated in the tumor by thephenomenon of co-option. Note that the blood vessels in the tumorsexpressing VEGF-A₁₆₅ only, are negative for glut-1 and, therefore, canbe considered to be newly formed.

FIG. 15: Western blots were generated with recombinant plexin D1ectodomains, expressed in E. coli and encompassing amino acids 47-506(lanes 1) or 225-388 (lanes 2). Serum of mouse 25 was tested before(Panel A) and after (Panel B) immunization with plexin D1 region 47-506.As shown in Panel B, the mouse immune serum specifically recognized E.coli recombinant protein 47-506 (52 kDa, lane 1) and the proteinencompassing plexin D1 residues 225-388 (a 18 kDa protein that liescompletely within the sequence that was used for immunization, lane 2).The pre-immune serum did not show such a reactivity (Panel A). Whentested in immunohistochemical stainings on a brain metastasis of analveolar soft tissue sarcoma, the mouse immune serum (Panel D), but notthe pre-immune serum (Panel C), showed positivity toward blood vesselsand tumor cells, a staining pattern that was similar to that ofsingle-domain antibody A12.

FIG. 16: Immunohistochemistry with monoclonal 1 μM antibodies, obtainedfrom B-lymphocytes from mouse 25. Antibodies 11F5H6 and 17E9C12 wereselected based on reactivity against protein 47-506 in ELISA, and wereanalyzed for their potential to detect plexin D1 in frozen sections ofhuman tumors. These antibodies showed strong positivity in brainmetastases of sarcoma and melanoma, as illustrated in the figure. Ofnote, the insets in Panels C-F represent control stainings in which theprimary antibody was omitted. Panels A and B show that these antibodiesdo not notably recognize vessel structures in normal brain tissue.

FIG. 17: Tumor homing of antibody 11F5H6. To further evaluate whethermonoclonal antibody 11F5H6 is able to recognize tumor blood vessels,angiogenic Me157-VEGF-A tumors were grown in brains of nude mice,essentially as described in Example 10. Antibody 11F5H6 (1 mg) wasinjected in a lateral tail vein and allowed to circulate for 15 minutes.After this period, the mice were anesthetized with 1.3% isoflurane andthe chest was opened, upon which a cardiac perfusion was performed with20 ml phosphate-buffered saline. After this procedure, mice weredecapitated, and brains removed and snap-frozen or fixed in formalin.Frozen sections of 4 μm were stained with anti-IgM antibody. In FIG. 17,Panel A, it is shown that antibody 11F5H6 homes to and accumulates intumor vessels but not in normal vessels (compare anti-IgM staining inPanel A with the anti-endothelial CD31 staining in Panel B). Suchstaining is not seen when performing anti-IgM staining on non-injectedmice. Thus, 11F5H6 is a promising antibody that allows tumor targeting.

FIG. 18: Expression of Plexin D1 in macrophages in a mouse model ofrheumatoid arthritis. Stainings were performed with single-domainantibody A12.

FIG. 19: expression of Plexin D1 in atherosclerosis. A subset ofmacrophages in human atherosclerotic plaques expresses plexin D1.Stainings were performed with single-domain antibody A12. A doublestaining was performed, displaying plexin D1 in red and the macrophagemarker CD68 in blue. A purple color indicates co-expression.

The tables show the following:

Table 1: Analysis of different pathologies for plexin D1 expression.

Table 2: Plexin D1 expression in melanocytic lesions increases frombenign to malignant lesions.

DETAILED DESCRIPTION EXAMPLES Example 1 Specific Expression of Plexin D1on Tumor-Associated Blood Vessels

Plexin D1 is expressed on neurons but also endothelial cells inangiogenic vessels during embryogenesis.

The present invention demonstrates that plexin D1 is expressed ontumor-associated blood vessels but not on normal blood vessels. This hasbeen shown by in situ hybridization of mouse brains, containingangiogenic human melanoma lesions (FIG. 2). The animal tumor model isdescribed in (B. Kusters et al., Cancer Res. 63:5408-5413 (2003)). Inshort, tumor cells are injected via a microsurgical procedure in theright carotid artery, resulting in tumor growth in the parenchyma of theright brain hemisphere. After three weeks, at the onset of neurologicalsymptoms, mice are sacrificed and brains removed and fixed in formalin.

Sections of 4 μm were subjected to in situ hybridization withdigoxigenin-labeled sense and antisense RNA fragments. RNA probes weregenerated by transcription using T3 and T7 RNA polymerase, respectively,from a PCR product, encompassing 600 bases in the 3′-untranslatedregion, and which was flanked by T7 and T3 promoters (Van der Zwaag etal. (2002), supra).

In situ hybridizations using antisense RNA probes and sense RNA probesas negative controls, were performed using standard protocols. Sectionswere deparaffinated by melting paraffin at 60° C. and subsequenttreatments with xylene and ethanol. After rehydration inphosphate-buffered saline (PBS), a proteinase K digestion was performed(10 μg/ml PBS in 20 mM Tris-HCl pH7.4/5 mM EDTA) for 15 minutes at 37°C. Sections were post-fixed in 4% buffered formaldehyde for 10 minutes,and acetylated in 0.1 M acetic acid anhydrid. Slides were washedsubsequently in 2×SSC (sodium Citrate/sodium chloride) and MILLIQ®.After drying, slides were hybridized with digoxigenin-labeled RNA probesovernight at 65° C. in 50% formamide/2×SSC.

High levels of plexin D1 RNA were observed in vessels of angiogenicMe157 tumors (FIG. 2) using a mouse-specific plexin D1 RNA probe. Tumorcells were also positive for the transcript. The non-perfect homologybetween mouse and human plexin D1 results in a weaker signal in thehuman tumor cells using the mouse probe.

Example 2 Expression of Plexin D1 in Tumors

To investigate plexin D1 RNA expression in human tumor samples, in situhybridizations were performed with a human-specific plexin D1 RNA probe.High plexin D1 RNA expression levels were found in a number of humantumors, including glioblastoma multiforme, brain metastases of sarcoma,renal cell carcinoma, adenocarcinoma of the colon and of the breast,both in tumor vasculature and tumor cells. A summary of plexinD1-expressing tumor types is given in Table 1. FIG. 3 shows someexamples of in situ hybridizations, e.g., a glioblastoma, a brainmetastasis of melanoma and a brain metastasis of colon carcinoma. PlexinD1 RNA was found not only on the tumor vasculature, but also excessivelyon the tumor cells themselves. Importantly as in FIG. 4, Panel A, noplexin D1 RNA expression is observed in normal brain vasculature. InFIG. 4, Panel B, a CD31 staining is shown, demonstrating that abundantvessels are present in these sections.

Example 3 Preparation on of Antibodies Against Plexin D1

To detect plexin D1 protein, antibodies were selected with affinitytoward plexin D1. To this end, a M13 pHENIX phage library wasconstructed expressing Llama single-domain V-H antibodies, constructedby RT-PCR from Llama B-lymphocytes as described (S. van Koningsbruggenet at., J. Immunol. Methods 279:149-161 (2003)). The population ofresulting cDNAs encoding V-H-single-domain antibody (sdab) fragments wasligated into phagemid vector pHENIXHis8VSV (results not shown),resulting in a fusion product with an 8*His-tag and a VSV-G-tag at theC-terminus. After electroporation in E. coli TG1 cells,ampicillin-resistant colonies were collected and pooled.

The resulting library had a complexity of 8×10⁸ clones. Eighty percentof plasmids contained full-length sdab insert as determined by PCRanalysis and immunological dot-blot-detection of the VSV-G-tag in sdabs(see below). The phage library was propagated as phagemids in E. coliTG1 bacteria. Phage particles were rescued by infection withtrypsin-sensitive helper phage M13K07 (50). Phages were purified andconcentrated from the culture supernatant by precipitation with 20%Polyethyleneglycol/2.5 M NaCl via standard methodology.

To select for phages, displaying antibodies with affinity toward plexinD1, immunotubes (Nunc, Roskilde, Denmark) were coated overnight at 4° C.with 5 μg/ml KLH-conjugated peptide (H₂N-ALEIQRRFPSPTPTNC-CONH₂ (SEQ IDNO:8), corresponding to amino acids 1-16 of the mature human PLXND1protein (accession no. AY116661) in 50 mM NaHCO₃ (pH 9.6). Of note, theglutamic acid on position 3 in this peptide is a lysine in the mousesequence; the remaining amino acids are homologous to mouse plxnd1.

After rigorous washing with PBS/0.05% TWEEN® 20 (PBST), non-specificbinding sites were blocked with 5% marvel in PBST (MPBST, 1 hour at roomtemperature (RT)) and 10¹³ phage particles from the library stock wereincubated with the immobilized peptide for 90 minutes at RT. Afterrigorous washing with PBST and PBS, bound phages were eluted by trypsintreatment (10 mg/ml, 30 minutes RT).

After trypsin inactivation with 1% newborn calf serum, the eluate wasused to infect log-phase TG1 cells to amplify PLXND1-binding phages andcalculate number of binders.

To enrich for binding phages, four rounds of selection were performed.From the second round on, selections were performed against unconjugatedpeptides, immobilized on DNA-binding plates (Costar) to preventselection of KLH-binders.

Individual PLXND1-binding phages with PCR-confirmed full-length sdabinserts were tested for specificity toward plexin D1. Wells ofDNA-binding plates or immunoplates (Nunc) were coated overnight at 4° C.with PLXND1-peptide or an irrelevant peptide (1 μg/well in PBS/0.5 MNaCl pH 9.0), Bovine serum albumin (1 μg/well in 50 mM NaHCO₃ pH 9.6) orhuman Immunoglobulin G (1 μg/well in 50 mM NaHCO₃ pH 9.6). Afterblocking non-specific binding sites with MPBST, wells were incubatedwith phages in MPBST for 1 hour at RT and non-bound phages removed byrigorous washing. Bound phages were detected using HRP-conjugatedanti-M13 (Amersham Pharmacia Biotech, Piscataway, N.J., USA) andtetramethylbenzidine (TMB; bioMerieux B.V., Netherlands). The reactionwas terminated with 2 M H₂SO₄ and enzymatic activity quantified bymeasuring absorbance at 450 nm using an ELISA reader.

Using this selection procedure, phages displaying V-H single-domainantibodies A12 and F8 on their surfaces were identified as specificbinders. FIG. 5, Panel A, shows that M13 phage-associated antibodies A12and F8 bind specifically to plexin D1 peptide, but not to bovine serumalbumin, immunoglobulins or an irrelevant peptide.

Expression of soluble single-domain antibodies was induced in log-phaseE. coli TG1 cells by culturing at 30° C. in 2×TYA medium/1 mM IPTG.Sdabs were collected by osmotic lysis using ice-cold TES buffer (200 mMTrisHCl, 0.5 mM EDTA, 500 mM sucrose) containing a protease inhibitorcocktail (Roche, Basel, Switzerland). Sdab concentrations were estimatedvia dot-blot analysis using the mouse monoclonal anti-VSV-G P5D4,alkaline phosphatase-conjugated rabbit anti-mouse immunoglobulin (Dako,Denmark) and NBT/BCIP staining. Sdabs were tested in ELISA forPLXND1-peptide specificity. Single-domain antibodies A12 and F8 did notbind to irrelevant peptide, not to bovine serum albumin, and not tohuman immunoglobin G (FIG. 5, Panel B). The dissociation constants (Kds)of the binding between single-domain antibodies A12 and F8 weredetermined using the Biacore 2000 (Uppsala, Sweden) biosensor. Thesensor chip and protein coupling chemicals were purchased from BiacoreAB. PLXND1-peptide-KLH conjugate (27 μg/ml in Na-Acetate, pH 4.0) or BSA(1 μg/ml in Na-Acetate, pH 5.0) was coupled to activated CM5 surfacesusing N-ethyl-N′-(dimethylaminopropyl) carbodiimide,N-hydroxysuccinimide, under conditions recommended by the manufacturer.Unreacted groups were inactivated by 1 M ethanolamine, pH 8.5.

Kinetic measurements were performed at 25° C. with a flow rate of 10ml/minute in HBS-EP buffer (10 mM Hepes, pH 7.4, 150 mM NaCl, 3 mM EDTA,0.005% surfactant P20).

Six concentrations of Ni-affinity-purified sdabs (in the range of 1 mMto 50 μM) were used to determine the dissociation constants (Kds) of theinteraction with the PLXND1-peptide. After each experiment, regenerationof the sensor surface was preformed with 10 mM NaOH. Specific binding,defined by binding to a PLXND1-surface minus binding to a controlBSA-surface, was analyzed using the BIAevaluation 4.1 software and a 1:1Langmuir binding model.

Affinities of single-domain antibodies A12 and F8 were 2.1×10⁻⁸ M and3.5×10⁻⁸ M, respectively (FIG. 6).

Example 4 Immunohistochemical Stainings with Single-domain AntibodiesA12 and F8

The single-domain antibodies are tagged at the carboxyterminal end witha VSV-His-tag, enabling immunohistochemical stainings using an anti-VSVantibody. The following protocol was followed for immunohistochemicalstainings with single-domain antibodies A12 and F8. Followingdeparaffinization, endogenous peroxidase activity was blocked byincubation with 0.03% H₂O₂. Antigen retrieval was performed by treatmentwith pronase according to standard protocols. Subsequently, slides werepre-incubated with normal horse or goat serum (to block non-specificbinding sites in sections of human and mouse tissues, respectively),followed by incubation with sdabs for 1 hour. Sdabs were detected bysequential 1-hour incubations with a mouse or rabbit anti-VSV-Gantiserum (Sigma-Aldrich Chemie B.V., Zwijndrecht, The Netherlands),biotinylated anti-mouse or anti-rabbit antibody as appropriate (Vector,Burlingame, Calif.), and avidin-biotin peroxidase complex (Vector,Burlingame, Calif.). Finally, peroxidase was visualized by the3-amino-9-ethylcarbazole (ScyTek, Utah, USA) peroxidase reaction withhematoxylin as counterstain. All steps were performed at RT.

The specificity of the antibody A12 and F8 for plexin D1 inimmunohistochemical stainings was first examined by staining mouseembryos in which expression patterns of plexin D1 on the RNA level werewell characterized (Van der Zwaag et al. (2002), supra), and comparingprofiles with immunostainings with anti-endothelial antibody anti-CD31(DAKO, Glostrup, Denmark). In growth plate of trabecular bone of miceembryos at E16.5, immunostaining was observed on CD31-positive bloodvessels. The staining profile correlated well to in situ hybridizationfor the plexin D1 transcript (FIG. 7, Panel A). The blood vessel originof PLXND1 expression was further confirmed by performing stainings onserial sections with sdabs and anti-human anti-CD31 antibody (anti-humanCD31).

Example 5 Staining of Tumor Cells with F8

Four μm sections cerebral mouse xenografts of the human melanoma cellline Me157-VEGF-A (Kusters et al. (2003), supra) were stained withsingle-domain antibody F8, according to the protocol exemplified inExample 4. The antibody clearly recognized plexin D1 on tumor bloodvessels (FIG. 7, Panel B). To further investigate plexin D1 proteinexpression on tumors, archival paraffin-embedded or tumor tissue ofdifferent origin (glioblastoma multiforme (FIG. 8, Panel A), brainmetastases of melanoma (FIG. 8, Panel B) colon carcinoma (FIG. 8, PanelC) and renal cell carcinoma (FIG. 8, Panel D) were immunostained withanti-PLXND1 sdabs. Immunohistochemistry using antibody A12 andcomparison with anti-human CD31 stainings on serial sections, showedexpression on all tumors examined and confirmed plexin D1 expression onthe protein level in tumor cells and in tumor blood vessels.

Example 6 Timing of Plexin Expression on Malignant Cells

To investigate whether expression of plexin D1 occurs on premalignantcells, a progression series of melanoma was stained, consisting ofbenign nevi, dysplastic nevi, radial growth phase melanoma, invasivemelanoma and disseminated melanoma. Melanocytes in benign nevi anddysplastic nevi do not express the protein, whereas malignantlytransformed cells, both in radial growth phase and vertical growth phasetumors are positive for the protein (FIG. 9 and Table 2).

Example 7 Activation State of Plexin D1-Expressing Cells

Plexin D1 expression is related to the activation state of theendothelial cells in tumor blood vessels. Treatment with ZD6474, aninhibitor of VEGFR2 and EGFR, was previously shown to block angiogenesisin a mouse brain tumor model, resulting in a phenotypic shift from anangiogenic to a non-angiogenic vessel co-opting phenotype (43).Treatment with ZD6474 resulted in a decrease of plexin D1 expression ontumor-associated blood vessels in a dose-dependent manner (FIG. 10).Thus, plexin D1 expression is a characteristic of activated endothelialcells.

Example 8 Immunohistochemistry with A12 on Normal Tissues

Expression of plexin D1 in normal brain, heart, skin, kidney, spleen,intestine, and endometrium was examined by immunohistochemistry usingantibody A12. Vessels in proliferative myometrium-expressed plexin D1,showing that plexin D1 is associated not only with pathologicalangiogenesis, but also with physiological angiogenesis (not shown).

In some instances, co-immunostainings were performed with the CD68macrophage marker. These stainings revealed that a subpopulation ofmacrophages expressed the protein (FIG. 11). Also, fibroblasts in skinand some proliferating intestinal epithelial cells were found to expressplexin D1 (not shown).

Example 9 Staining of Macrophages in Inflammatory Diseases

To further examine the involvement of plexin D1 in diseases withprominent macrophage involvement, immunohistochemical stainings werepreformed on atherosclerotic plaques, multiple sclerosis and rheumatoidarthritis. Macrophages express plexin D1.

Example 10 Access to Plexin D1 in Tumor Vessels Via IntravenousInjection

The expression of plexin D1 protein on tumor blood vessels suggests thatplexin D1 is accessible via intravenous injection. To test this, 2×10⁵stably transfected Me157 cells expressing the VEGF-A₁₆₅ isoform weremicrosurgically injected into the right internal carotid artery ofBALB/C nude mice. After 18 days, when animals showed neurologicalsymptoms (Kusters et al. (2003), supra), 10¹² PLXND1-binding phages ofclones A12, F8 or non-relevant phages were injected in the tail vein ofnude mice, carrying established Me157-VEGF-A₁₆₅ brain metastases (n=2for A12, n=4 for F8, n=3 for control phage).

In two other groups of mice, 30 μg sdab F8 or a control sdab (n=2 foreach group) was intravenously injected. After 5 minutes, mice wereanesthetized using isoflurane, the chests were opened, and non-boundphages were washed from the system by cardiac perfusion with 15 ml ofphosphate-buffered saline (PBS). Then, mice were sacrificed by cervicaldislocation, and parts of brains, hearts, lungs, livers, spleens andkidneys were snap frozen in liquid nitrogen.

Other parts were fixed in formalin to be paraffin-embedded. After shorthematoxylin staining, tumors were dissected from 10 μm brain sectionsusing laser capture dissection microscopy (Leica laser dissectionmicroscope). Equivalent areas were dissected from unaffected brain,contralateral to the tumor.

Subsequently, phages were eluted from dissected tissue samples usingtrypsin treatment and used to infect TG1 cells. Numbers ofcolony-forming phages were counted and used as a measure of tumorhoming. To qualitatively assess tumor homing by phages or sdabs, 4sections, serial to the sections used for laser dissection, were stainedwith anti-M13 p8 antibody (Abcam Limited, Cambridge, UK) to detect boundphages, or anti-VSV-G antibodies (Sigma-Aldrich) to detect single-domainantibodies.

Intravenous injection of M13 phages displaying anti-PLXND1 single-domainantibody F8, but not phages carrying irrelevant single-domainantibodies, in mice carrying angiogenic melanoma lesions resulted inaccumulation of phages in tumor vessels but not to detectable specificpresence of phages in normal brain vessels, nor blood vessels in liver,spleen, kidney (FIG. 12, Panels A and D, not shown). This indicates thatplexin D1 is expressed at the luminal side of the endothelial cellspecifically in tumor blood vessels and thus can be used as a targetablemarker.

Injection of the partially purified single-domain antibody accordinglyled to preferential tumor localization (FIG. 12, Panel C). In the lattersituation, it must be considered that the small molecular weight of 20kDa of the single-domain antibodies enable extravasation from the highlypermeable tumor vessels and accumulation in the tumor interstitium. Thislatter effect is non-specific and is also observed with non-relevantsingle-domain antibodies. It is envisioned that antibodies of smallmolecular weight and relatively low affinities have higher penetrabilitythrough tumors and are more suitable for targeting the tumor cellcompartment.

Example 11 Accumulation of F8 in Tumor Blood Vessels

Mice were injected transcranially with E98, a glioma xenograft line. E98tumors are maintained as subcutaneous tumors. A Balbc/c nu/nu athymicmouse carrying a subcutaneous E98 tumor was killed and the tumorremoved. The tumor was minced with a sterile scalpel and the homogenatewas passed through a sterile 70 μm mesh nylon filter. Twenty μl of theresulting cell suspension, containing 150,000 cells, was injectedtranscranially in the brain of nude mice. After 3 weeks, M13 phagesdisplaying single-domain antibody F8 were injected intravenously, andafter five minutes the mouse was subjected to cardiac perfusion with 15ml of phosphate-buffered saline.

The mice were killed, brains removed and fixed in formalin. Four μmsections were subjected to immunohistochemistry with anti-M13 antibody,and serial sections were stained immunohistochemically with antibodiesagainst CD34 (endothelial marker) and glut-1 (a marker for pre-existentbrain endothelial cells (B. Kusters et al., Cancer Res. 62:341-345(2002)).

Phages carrying anti-plexin D1 single-domain antibodies accumulatedspecifically in tumor-associated blood vessels, but not in normalvessels (FIG. 13). Importantly, phages also accumulated in tumor bloodvessels that were positive for glut-1, and that, therefore, can beconsidered as pre-existent blood vessels, rather than newly formed bloodvessels. This indicates that not only angiogenic blood vessels aresubject to targeting with anti-plexin D1 antibodies, but alsonon-angiogenic, yet activated blood vessels in tumors.

Example 12 Recombinant Plexin D1 Ectodomains Inhibit Angiogenesis

Human melanoma Me157 cells were transfected with the VEGF-A₁₆₅ codingsequence in vector pIREShyg. Stably transfected cells were selected byculturing in 200 μg/ml hygromycin in Dulbecco's Modified Eagle medium(DMEM) supplemented with 10% fetal calf serum (FCS) andpenicillin/streptomycin. Because expression of the hygromycin resistancegene is linked to that of the VEGF-A cDNA via the internal ribosomalentry site (IRES), all hygromycin-resistant cells will produce theVEGF-A protein also. Stably transfected Me157-VEGF cells weresubsequently transfected with pIRESnco-PlexinD1 ED. The vector containsthe cDNA encoding the extracellular domain from nucleotides 1-2745,linked via the IRES to expression of the neomycin resistance gene.

Double transfectants were injected in the right carotid artery of nudemice, and tumors were allowed to develop. At the onset of neurologicalsymptoms (approximately 18 days) mice were subjected toGadolinium-DTPA-enhanced magnetic resonance imaging. Subsequently, micewere sacrificed, brains fixed in formalin and subjected toimmunohistochemical stainings to examine the tumor vasculature.

When compared to controls, consisting of tumors expressing VEGF-A only,Gd-DTPA enhancement in T1-weighted magnetic resonance imaging (MRI) wasless (compare FIG. 14, Panel A, representing two examples ofMe157-VEGF-A₁₆₅ tumors, with Panel B representing two examples ofMe157-VEGF-A₁₆₅/PLEXIND1-ED tumors. In the tumors expressing VEGF-A₁₆₅and Plexin D1 ectodomain, vasculature shows upregulation of theendothelial marker CD34 (a hallmark of endothelial activation byVEGF-A₁₆₅). The vasculature in tumors expressing VEGF-A₁₆₅ only isnegative for the brain endothelial cell marker glut-1, which isconsistent with the fact that these vessels are newly made and,therefore, lack brain-endothelial cell-specific markers. As can be seenin FIG. 12, Panel B, the vessels that are associated with tumors thatexpress the plexin D1 ectodomain too, do express glut-1. This is astrong indication that these vessels are actually pre-existent. Thus,the plexin D1 ectodomain does not prevent activation of endothelialcells by VEGF-A₁₆₅, but it does prevent the formation of neovasculature.

Example 13 High-Affinity Antibodies Against Plexin D1

A protein sequence, corresponding to amino acids 47-506 (the 459 mostamino terminal amino acids of the mature protein), was expressed in E.coli M15 pREP4 cells, using the expression vecor pQE16 (Qiagen). Therecombinant protein, which was produced in the bacterial cells asinclusion bodies, was dissolved in denaturing buffer, containing 4 Murea and 1 mM dithiothreitol (DTT) and afterwards gradually dialyzedagainst PBS. The protein was used to immunize BALB c/c mouse 25according to standard procedures.

FIG. 15 shows the characteristics of the mouse serum. As shown in FIG.15, Panel B, the mouse immune serum specifically recognized E. colirecombinant protein 47-506 (52 kDa, lane 1), and a second recombinantplexin D1 sequence of 18 kDa, comprising amino acids 225-388 (thus lyingcompletely within the sequence that was used for immunization, lane 2).The pre-immune serum did not show such a reactivity (Panel A).

When tested in immunohistochemical stainings on a brain metastasis of analveolar soft tissue sarcoma, the mouse immune serum (Panel D), but notthe pre-immune serum (Panel C), showed positivity toward blood vesselsand tumor cells, a staining pattern that was similar to that ofsingle-domain antibody A12. Thus, the B-lymphocytes of this mouse wereconsidered suitable to generate hybridomas of spleen B-lymphocytes withmyeloma cell line SP2/0.

From these hybridomas, a number of antibody-producing cell lines wereselected based on reactivity against protein 47-506 in ELISA, and wereanalyzed for their potential to detect plexin D1 in frozen sections ofhuman tumors. Of these, 11F5 H6 and 17E9C12, both antibodies of the IgMsubtype, showed strong positivity in brain metastases of sarcoma andmelanoma, as illustrated in FIG. 16. The insets in Panels C-F representcontrol stainings in which the primary antibody was omitted. Panels Aand B show that these antibodies do not notably recognize vesselstructures in normal brain tissue.

Example 14 Monoclonal Antibody 11F5H6 is Able to Recognize Tumor BloodVessels

To further evaluate whether monoclonal antibody 11F5H6 is able torecognize tumor blood vessels, angiogenic Me157-VEGF-A tumors were grownin brains of nude mice, essentially as described in Example 10. Antibody11F5H6 (1 mg) was injected in a lateral tail vein and allowed tocirculate for 15 minutes. After this period, the mice were anesthetizedwith 1.3% isoflurane and the chest was opened, upon which a cardiacperfusion was performed with 20 ml phosphate-buffered saline.

After this procedure, mice were decapitated, and brains removed andsnap-frozen or fixed in formalin. Frozen sections of 4 μm were stainedwith anti-IgM antibody. In FIG. 17, Panel A, it is shown that antibody11F5H6 homes to and accumulates in tumor vessels but not in normalvessels (compare anti-IgM staining in FIG. 17, Panel A, with theanti-endothelial CD31 staining in FIG. 17, Panel B). Such staining isnot seen when performing anti-IgM staining on non-injected mice. Thus,11F5H6 is a promising antibody that allows tumor targeting.

Example 15 Plexin D1 Expression in Rheumatoid Arthritis

Plexin D1 is expressed in macrophages in mouse models of rheumatoidarthritis (FIG. 18). A subset of macrophages in human atheroscleroticplaques also expresses plexin D1 (FIG. 19). Stainings were performedwith single-domain antibody A12. In FIG. 19, a double staining wasperformed, displaying plexin D1 in red and the macrophage marker CD68 inblue. A purple color indicates co-expression.

Sequences A12 (SEQ ID NO: 1):ATGAAATACCTATTGCCTACGGCAGCCGCTGGATTGTTATTACTCGCGGCCCAGCCGGCCATGGCCCAGGTGCAGCTGCAGGAGTCTGGGGGAGGCTTGGTGCAGCCTGGGGGGTCTCTGAGACTCTCCTGTGCAGCCTCTGGAAGCAGTATCAGTATCAATAACTGGGGCTGGTACCGCCAGGCTCCAGGAAAACAGCGCGAGCGGGTCGCAGCTATATCTGGTGGTAAAACAGTCTATGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGGTGTATCTGCAAATGAACAGCCTGAAACCTGAGGATACGGCCGTCTATTACTGTAGAGCAGTCCGGAAAAGTACGGGTTGGCTTAGGGGGCTTGACGTCTGGGGCCAGGGGACCCAGGTCACCGTCTCCGCAGAACCCAAGACACCAAAACCACAACCAGCGGCCGCACATCATCACCATCATCACCATCATTATACAGACATAGAGATGAACCGACTTGGAAAGGGGGCCGCATAG A12 protein sequence (SEQ ID NO: 2)MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGSSISINNWGWYRQAPGKQRERVAAISGGGKTVYADSVKGRITISRDNAKNTVYLQMNSLKPEDTAVYYCRAVRKSTGWLRGLDVWGQGTQVTVSAEPKTPKPQPAAAHHHHHHHHYTDIEMNRLGKGAA@ F8 (SEQ ID NO: 3):ATGAAATACCTATTGCCTACGGCAGCCGCTGGATTGTTATTACTCGCGGCCCAGCCGGCCATGGCCCAGGTGCAGCTGCAGGAGTCTGGGGGAGGATTGGTGCAGGCTGGAGACTCTCTGAGACTCTCCTGTGCAGCCTCTGGACGCACCTTCAGTACTTTGATTATGGCCTGGTTCCGCCAGGCTCCAGGGAAGGAGCGTGAATTTGTAGCGGCGATTAGCCGGGGTGGCGGTAGCACAAGCTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACGCGGTGTATCTACAAATGAACAGCCTGAAACCTGATGACACGGCCGTCTATTACTGTAATGCCCGGTACGGTAGCCGAATTTACTGGGGCCAGGGGACCCAGGTCACCGTCTCCTCAGAACCCAAGACACCAAAACCACAACCAGCGGCCGCACATGATCACCATCATCACCATCATTATACAGACATAGAGATGAACCGACT TGGAAAGGGGGCCGCATAGF8 protein sequence (SEQ ID NO: 4)MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQAGDSLRLSCAASGRTFSTLIMAWFRQAPGKEREFVAAISRGGGSTSYADSVKGRFTISRDNSKNAVYLQMNSLKPDDTAVYYCNARYGSRIYWGQGTQVTVSSEPKTPKPQPAAAHHHHHHHHYTDIEMNRLGKGAA@ Sequence single chain antibody, derived fromantibody 11F5H6 (SEQ ID NO: 5)MKYLLPTAAAGLLLLAAQPAMADYKDIVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVFNRLSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLITGAGTKLELKRGGGGSGGGGSGGGGRAPGGGGSEVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWIGLINPYNGGTSYNQKFKGKATLTVDKSSSTAYMELLSLTSEDSAVYYCARAITTDGWFAYWGQGTLVTVSAAAAHHHHHHHHYTDIEMNRLG KGAASequence single chain antibody, derived fromantibody 17EC12 (SEQ ID NO: 6)MKYLLPTAAAGLLLLAAQPAMADYKDIQMTQTPSSLAVSAGEKVTMSCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFFGSGSGTDFTLTISSVQAEDLAVYYCHQYLSSWTFGGGTKLEIKRGGGGSGGGGSGGGGSGGGGSQVQLQQSGAEINKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAMDYWGQGTSVTVSSAAAHHHHHHHHYTDIEMNRLGKGAA

TABLE 1 PLXND1 expression in human tissues Tissue PLXND1 expressionMalignant Adenocarcinoma of oesophagus (n = 1) Tumor vessels and tumorcells Adenocarcinoma of rectum (n = 5) Tumor vessels, tumor cells andmacrophages Adenocarcinoma of prostate (n = 1) Tumor vessels and tumorcells Alveolar soft part sarcoma of femur (n = 1) Tumor vessels andtumor cells Astrocytoma (n = 1) Tumor vessels Carcinoid tumor of lung (n= 1) Tumor vessels, tumor cells and macrophages Ductal carcinoma in situof mamma (n = 5) Tumor vessel, tumor cells, macrophages, fibroblastsFollicular lymphoma (n = 8) Tumor vessels Glioblastoma Multiforme (n =3) Tumor vessels and tumor cells Brain metastasis of adenocarcinoma (n =4) (mamma, lung, rectum) Tumor vessels and tumor cells Brain metastasisof alveolar soft part sarcoma (n = 1) Tumor vessels and tumor cellsBrain metastasis of renal cell carcinoma (n = 1) Tumor vessels and tumorcells Liver metastasis of adenocarcinoma colon (n = 2) Tumor vessels,tumor cells and macrophages Lobular carcinoma in situ of mamma (n = 3)Tumor vessels and tumor cells weakly positive, macrophages andfibroblasts Lymph node metastasis ductal mamma carcinoma (n = 1) Tumorcells and some tumor vessels Ovary metastasis of adenocarcinoma colon (n= 1) Tumor cells and myofibroblasts Renal cell carcinoma (n = 1) Tumorvasculature and tumor cells Urothelial cell carcinoma of prostate (n =2) Tumor vessel, tumor cells and macrophages Non-malignant Bladder (n= 1) Macrophages Blood vessel, atherosclerosis (n = 6) Macrophages Bonemarrow (n = 2) Brain cortex (n = 1) Some neurons perinuclear Brain,Alzheimer + CAA (n = 1) Endometrium Proliferation phase (n = 5)Macrophages Secretion phase (n = 4) Macrophages Secretion/menstruationphase (n = 1) Macrophages Endometriosis interna (n = 1) MacrophagesHeart (n = 1) Some muscle cells perinuclear Large intestine (n = 1) Someluminal staining of epithelium, macrophages, fibroblasts Liver (n = 1)Liver cells perinuclear granular, macrophages Lung (n = 2) MacrophagesMamma (n = 2) Some epithelial cells perinuclear Mamma, ductalhyperplasia (n = 1) Focal epithelial cells perinuclear, macrophagesOesophagus (n = 1) Macrophages Small intestine (n = 1) Some luminalstaining of epithelium macrophages, fibroblasts Spleen (n = 1)Macrophages

TABLE 2 PLXND1 expression in melanoma progression series Absent ModerateAbundant Naevocellular naevi (n = 18) 18 Atypical naevi (n = 14) 14Melanomas in situ (n = 5) 5 Primary melanomas (n = 26) 4 2 20 Melanomametastases Lymph node (n = 9) 1 2 6 Skin (n = 5) 1 1 3 Brain (n = 5) 5Lung (n = 1) 1

1.-38. (canceled)
 39. A method for detecting the expression of plexinD1, the method comprising: providing a sample from a subject comprisingtumor cells and/or activated macrophages; contacting the sample with anantibody or antibody fragment specific for plexin D1 in vitro; anddetecting binding of the antibody or antibody fragment to the tumorcells and/or activated macrophages.
 40. The method according to claim39, wherein the tumor cells are from a tumor selected from the groupconsisting of brain tumors, astrocytomas, oligodendrogliomas,hemangioblastomas, colon carcinomas, ductal carcinomas of the colon,prostate carcinomas, renal cell carcinomas, renal clear cell carcinomas,ovary carcinomas, squamous cell carcinomas, melanomas, lung carcinomas,small-cell lung carcinomas, non-small cell lung carcinomas, and softtissue sarcomas.
 41. The method according to claim 39, wherein the tumorcells are from a tumor selected from the group consisting of prostatecarcinomas, renal cell carcinomas, renal clear cell carcinomas, ovarycarcinomas, squamous cell carcinomas, melanomas, lung carcinomas,small-cell lung carcinomas, non-small cell lung carcinomas, and softtissue sarcomas.
 42. The method according to claim 39, wherein thebinding of the antibody or the antibody fragment to the tumor cellsand/or activated macrophages indicates the presence of a disorderselected from the group consisting of brain tumors, astrocytomas,oligodendrogliomas, hemangioblastomas, colon carcinomas, ductalcarcinomas of the colon, prostate carcinomas, renal cell carcinomas,renal clear cell carcinomas, ovary carcinomas, squamous cell carcinomas,melanomas, lung carcinomas, small-cell lung carcinomas, non-small celllung carcinomas, and soft tissue sarcomas.
 43. The method according toclaim 39, wherein the binding of the antibody or the antibody fragmentto the tumor cells and/or activated macrophages indicates the presenceof a disorder selected from the group consisting of prostate carcinomas,renal cell carcinomas, renal clear cell carcinomas, ovary carcinomas,squamous cell carcinomas, melanomas, lung carcinomas, small-cell lungcarcinomas, non-small cell lung carcinomas, and soft tissue sarcomas.44. The method according to claim 39, wherein the antibody or antibodyfragment is labeled with a detectable marker.
 45. The method accordingto claim 44, wherein the detectable marker is selected from the groupconsisting of a radioactive label, a paramagnetic label, a fluorescentlabel, and a chemiluminescent label.
 46. The method according to claim39, wherein the sample is from bodily tissue or fluid.
 47. The methodaccording to claim 39, wherein the tumor cells are ovarian carcinomacells.